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- PDB-1oby: Crystal structure of the complex of PDZ2 of syntenin with a synde... -

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Basic information

Entry
Database: PDB / ID: 1oby
TitleCrystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.
Components
  • SYNDECAN-4
  • SYNTENIN 1
KeywordsCELL ADHESION / ADHESION-COMPLEX / PDZ DOMAIN / SIGNAL TRANSDUCTION / NUCLEAR PROTEIN
Function / homology
Function and homology information


Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / interleukin-5 receptor complex / HS-GAG biosynthesis / interleukin-5 receptor binding ...Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / interleukin-5 receptor complex / HS-GAG biosynthesis / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / inner ear receptor cell stereocilium organization / HS-GAG degradation / syndecan binding / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / costamere / negative regulation of receptor internalization / frizzled binding / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / ureteric bud development / Syndecan interactions / thrombospondin receptor activity / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / RSV-host interactions / Respiratory syncytial virus (RSV) attachment and entry / fibronectin binding / positive regulation of focal adhesion assembly / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / Retinoid metabolism and transport / cell adhesion molecule binding / ionotropic glutamate receptor binding / positive regulation of stress fiber assembly / negative regulation of T cell proliferation / ephrin receptor binding / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / lysosomal lumen / regulation of mitotic cell cycle / protein kinase C binding / Cell surface interactions at the vascular wall / adherens junction / neural tube closure / positive regulation of JNK cascade / wound healing / Regulation of necroptotic cell death / Golgi lumen / azurophil granule lumen / melanosome / cell migration / extracellular vesicle / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / blood microparticle / Ras protein signal transduction / cytoskeleton / Attachment and Entry / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / PDZ domain / Pdz3 Domain ...Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Syntenin-1 / Syndecan-4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2003
Title: Molecular Roots of Degenerate Specificity in Syntenin'S Pdz2 Domain: Reassessment of the Pdz Recognition Paradigm
Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
History
DepositionJan 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYNTENIN 1
B: SYNTENIN 1
P: SYNDECAN-4
Q: SYNDECAN-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5657
Polymers18,2774
Non-polymers2883
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.337, 54.441, 50.219
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

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Components

#1: Protein SYNTENIN 1 / SYNDECAN BINDING PROTEIN 1 / MELANOMA DIFFERENTIATION ASSOCIATED PROTEIN-9 / MDA-9 / SCAFFOLD ...SYNDECAN BINDING PROTEIN 1 / MELANOMA DIFFERENTIATION ASSOCIATED PROTEIN-9 / MDA-9 / SCAFFOLD PROTEIN PBP1 / TACIP18 / PRO-TGF-ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18


Mass: 8394.598 Da / Num. of mol.: 2 / Fragment: PDZ2, RESIDUES 197-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O00560
#2: Protein/peptide SYNDECAN-4 / AMPHIGLYCAN / SYND4 / RYUDOCAN CORE PROTEIN


Mass: 743.761 Da / Num. of mol.: 2 / Fragment: LAST 6 RESIDUES, RESIDUES 193-198 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P31431
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL ...MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL TRANSCRIPTION PROTEINS OR SIGNALING COMPONENTS. ALSO SEEMS TO COUPLE FACTOR SOX4 TO THE IL-5 RECEPTOR (IL5RA) MOL_ID 2: CELL SURFACE PROTEOGLYCAN CONTAINING HEPARAN SULFATE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49.7 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.8
Details: SITTING DROP WITH 0.1 M HEPES, PH 6.8, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, AND 0.2 MGSO4
Crystal grow
*PLUS
Temperature: 294 K / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MHEPES1reservoirpH6.8
21.6 Mammonium sulfate1reservoir
320 mM1reservoirCoCl2
40.2 M1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 31, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 46421 / % possible obs: 97.4 % / Redundancy: 3.57 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.8
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.86 / % possible all: 83.7
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Num. obs: 12987 / Num. measured all: 46421 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 83.7 % / Num. unique obs: 1108 / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.86

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N99

1n99


Resolution: 1.85→49.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.645 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 985 7.6 %RANDOM
Rwork0.175 ---
obs-12001 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0.68 Å2
2--0.44 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 15 145 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211235
X-RAY DIFFRACTIONr_bond_other_d0.0010.021118
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9461663
X-RAY DIFFRACTIONr_angle_other_deg0.94132610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021342
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02222
X-RAY DIFFRACTIONr_nbd_refined0.2040.2227
X-RAY DIFFRACTIONr_nbd_other0.2570.21273
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6680.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3660.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.121.5787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00521275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.163448
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0054.5388
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 55
Rwork0.259 739
Refinement TLS params.

T33: 0.0164 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32040.596-1.75432.7056-0.61484.8398-0.0471-0.0468-0.0891-0.1466-0.0233-0.0417-0.17670.16820.07050.08390.0029-0.00460.10130.00438.5350.03311.409
21.1031-0.63781.20351.819-0.66514.9443-0.0677-0.03250.02110.0309-0.1043-0.04750.27790.09630.1720.1082-0.00290.04120.10330.00748.83930.56312.219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A197 - 270
2X-RAY DIFFRACTION2B197 - 270
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.82

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